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Blood extracellular vesicles carrying brain-specific mRNAs are potential biomarkers for detecting gene expression changes in the female brain

Molecular Psychiatry (2024)Cite this article

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Abstract

The absence of non-invasive tests that can monitor the status of the brain is a major obstacle for psychiatric care. In order to address this need, we assessed the feasibility of using tissue-specific gene expression to determine the origin of extracellular vesicle (EV) mRNAs in peripheral blood. Using the placenta as a model, we discovered that 26 messenger RNAs that are specifically expressed in the placenta are present in EVs circulating in maternal blood. Twenty-three of these transcripts were either exclusively or highly expressed in maternal blood during pregnancy only and not in the postpartum period, verifying the feasibility of using tissue-specific gene expression to infer the tissue of origin for EV mRNAs. Using the same bioinformatic approach, which provides better specificity than isolating L1 cell-adhesion molecule containing EVs, we discovered that 181 mRNAs that are specifically expressed in the female brain are also present in EVs circulating in maternal blood. Gene set enrichment analysis revealed that these transcripts, which are involved in synaptic functions and myelination, are enriched for genes implicated in mood disorders, schizophrenia, and substance use disorders. The EV mRNA levels of 13 of these female brain-specific transcripts are associated with postpartum depression (adjusted p-vals = 3 × 10−5 to 0.08), raising the possibility that they can be used to infer the state of the brain. In order to determine the extent to which EV mRNAs reflect transcription in the brain, we compared mRNAs isolated from cells and EVs in an iPSC-derived brain microphysiological system differentiated for 3 and 9 weeks. We discovered that, although cellular and extracellular mRNA levels are not identical, they do correlate, and it is possible to extrapolate cellular RNA expression changes in the brain via EV mRNA levels. Our findings bring EV mRNAs to the forefront of peripheral biomarker development efforts in psychiatric diseases by demonstrating the feasibility of inferring transcriptional changes in the brain via blood EV mRNA levels.

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Fig. 1: Summary of experiments.
Fig. 2: Placenta specific gene mRNAs in blood are present at high levels during the pregnancy but not the postpartum period.
Fig. 3: Proteins used for neural derived EV isolation lack brain specificity.
Fig. 4: Brain specific EV mRNAs in blood associate with postpartum depression.
Fig. 5: Brain organoid characterization.
Fig. 6: Cellular and EV mRNA levels are correlated in bMPS organoids.

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Code availability

The R code used for the analysis in this manuscript is available upon request.

Data availability

The sequencing data is available from the NCBI Sequence Read Archive under Bioproject PRJNA1006349.

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Acknowledgements

The authors would like to thank Ms. Ou Chen for her technical help. This study was funded by the Stanley Medical Research Institute and the following NIH grants NIH-NIMH R01 MH112704, NIH-NIMH 1K23 MH110607 R01ES034554. The authors acknowledge the Integrated Imaging Center and the Advanced Research Computing at Hopkins (ARCH) core facility at Johns Hopkins University. This publication was partially developed under Assistance Agreement No RD83950501 awarded by the U.S. EPA to LS. It had not been formally reviewed by EPA. The views expressed in the publication are solely those of LS and co-authors and do not necessarily reflect those of the Agency. EPA does not endorse any products or commercial services mentioned in this publication.

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Authors and Affiliations

  1. Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA

    Lena Smirnova, Sergio Modafferi & Charlotte Schlett

  2. Departments of Obstetrics & Gynecology and of Psychiatry, Weill Cornell Medicine, New York, NY, USA

    Lauren M. Osborne

  3. Department of Psychiatry and Neurobehavioral Sciences, University of Virginia, Charlottesville, VA, USA

    Jennifer L. Payne

  4. Department of Pediatrics, Johns Hopkins School of Medicine, Baltimore, MD, USA

    Sarven Sabunciyan

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Contributions

LS, LMO, JLP and SS conceived the idea and designed the initial experiments. LS, SM, CS performed the bMPS experiments. LMO and JLP collected the postpartum depression samples, characterized the patients and selected the cohorts used in the study. SS performed the EV assays, constructed NGS libraries and performed bioinformatic analysis. Everyone was involved in data interpretation and writing of the paper.

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Correspondence to Sarven Sabunciyan.

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Competing interests

JLP has served as a consultant for SAGE Therapeutics, Brii Biosciences, and Pure Tech Health. JLP has received an honorarium from Karuna Therapeutics for speaking to the company. JLP owns a patent entitled “Epigenetic Biomarkers of Postpartum Depression.” The other authors declare no competing interests.

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Smirnova, L., Modafferi, S., Schlett, C. et al. Blood extracellular vesicles carrying brain-specific mRNAs are potential biomarkers for detecting gene expression changes in the female brain. Mol Psychiatry (2024). https://doi.org/10.1038/s41380-023-02384-6

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